1
|
Cantallops Vilà P, Ravichandra A, Agirre Lizaso A, Perugorria MJ, Affò S. Heterogeneity, crosstalk, and targeting of cancer-associated fibroblasts in cholangiocarcinoma. Hepatology 2024; 79:941-958. [PMID: 37018128 DOI: 10.1097/hep.0000000000000206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 11/25/2022] [Indexed: 04/06/2023]
Abstract
Cholangiocarcinoma (CCA) comprises diverse tumors of the biliary tree and is characterized by late diagnosis, short-term survival, and chemoresistance. CCAs are mainly classified according to their anatomical location and include diverse molecular subclasses harboring inter-tumoral and intratumoral heterogeneity. Besides the tumor cell component, CCA is also characterized by a complex and dynamic tumor microenvironment where tumor cells and stromal cells crosstalk in an intricate network of interactions. Cancer-associated fibroblasts, one of the most abundant cell types in the tumor stroma of CCA, are actively involved in cholangiocarcinogenesis by participating in multiple aspects of the disease including extracellular matrix remodeling, immunomodulation, neo-angiogenesis, and metastasis. Despite their overall tumor-promoting role, recent evidence indicates the presence of transcriptional and functional heterogeneous CAF subtypes with tumor-promoting and tumor-restricting properties. To elucidate the complexity and potentials of cancer-associated fibroblasts as therapeutic targets in CCA, this review will discuss the origin of cancer-associated fibroblasts, their heterogeneity, crosstalk, and role during tumorigenesis, providing an overall picture of the present and future perspectives toward cancer-associated fibroblasts targeting CCA.
Collapse
Affiliation(s)
| | - Aashreya Ravichandra
- Medical Clinic and Polyclinic II, Klinikum Rechts Der Isar, Technical University Munich, Munich, Germany
| | - Aloña Agirre Lizaso
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV-EHU), Donostia-San Sebastian, Spain
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Research Institute, Donostia University Hospital, University of the Basque Country (UPV-EHU), Donostia-San Sebastian, Spain
- CIBERehd, Institute of Health Carlos III, Madrid, Spain
- Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Silvia Affò
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| |
Collapse
|
2
|
Pathak S, Singh V, Kumar N, Jayandharan GR. Inducible caspase 9-mediated suicide gene therapy using AAV6 vectors in a murine model of breast cancer. Mol Ther Methods Clin Dev 2023; 31:101166. [PMID: 38149057 PMCID: PMC10750187 DOI: 10.1016/j.omtm.2023.101166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/20/2023] [Indexed: 12/28/2023]
Abstract
Breast carcinoma has one of the highest incidence rates (11.7%), with significant clinical heterogeneity. Although conventional chemotherapy and surgical resection are the current standard of care, the resistance and recurrence, after these interventions, necessitate alternate therapeutic approaches. Cancer gene therapy for breast cancer with the suicide gene is an attractive option due to their directed delivery into the tumor. In this study, we have developed a novel treatment strategy against breast cancer with recombinant adeno-associated virus (AAV) serotype 6 vectors carrying a suicide gene, inducible Caspase 9 (iCasp9). Upon treatment with AAV6-iCasp9 vectors and the chemical inducer of dimerizer, AP20187, the viability of murine breast cancer cells (4T1) was significantly reduced to ∼40%-60% (mock control 100%). Following intratumoral delivery of AAV6-iCasp9 vectors in an orthotopic breast cancer mouse model, we observed a significant increase in iCasp9 transgene expression and a significant reduction in tumor growth rate. At the molecular level, immunohistochemical analysis demonstrated subsequent activation of the effector caspase 3 and cellular death. These data highlight the potential of AAV6-iCasp9-based suicide gene therapy for aggressive breast cancer in patients.
Collapse
Affiliation(s)
- Subhajit Pathak
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Center for Engineering in Medicine and Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Vijayata Singh
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Center for Engineering in Medicine and Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Narendra Kumar
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Center for Engineering in Medicine and Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Giridhara R. Jayandharan
- Laurus Center for Gene Therapy, Department of Biological Sciences and Bioengineering and Mehta Family Center for Engineering in Medicine and Gangwal School of Medical Sciences and Technology, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| |
Collapse
|
3
|
Kumari S, Gupta R, Ambasta RK, Kumar P. Emerging trends in post-translational modification: Shedding light on Glioblastoma multiforme. Biochim Biophys Acta Rev Cancer 2023; 1878:188999. [PMID: 37858622 DOI: 10.1016/j.bbcan.2023.188999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 10/21/2023]
Abstract
Recent multi-omics studies, including proteomics, transcriptomics, genomics, and metabolomics have revealed the critical role of post-translational modifications (PTMs) in the progression and pathogenesis of Glioblastoma multiforme (GBM). Further, PTMs alter the oncogenic signaling events and offer a novel avenue in GBM therapeutics research through PTM enzymes as potential biomarkers for drug targeting. In addition, PTMs are critical regulators of chromatin architecture, gene expression, and tumor microenvironment (TME), that play a crucial function in tumorigenesis. Moreover, the implementation of artificial intelligence and machine learning algorithms enhances GBM therapeutics research through the identification of novel PTM enzymes and residues. Herein, we briefly explain the mechanism of protein modifications in GBM etiology, and in altering the biologics of GBM cells through chromatin remodeling, modulation of the TME, and signaling pathways. In addition, we highlighted the importance of PTM enzymes as therapeutic biomarkers and the role of artificial intelligence and machine learning in protein PTM prediction.
Collapse
Affiliation(s)
- Smita Kumari
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India
| | - Rohan Gupta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India; School of Medicine, University of South Carolina, Columbia, SC, United States of America
| | - Rashmi K Ambasta
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India; Department of Biotechnology and Microbiology, SRM University, Sonepat, Haryana, India.
| | - Pravir Kumar
- Molecular Neuroscience and Functional Genomics Laboratory, Department of Biotechnology, Delhi Technological, University, India.
| |
Collapse
|
4
|
Li Y, Zhou H, Liu P, Lv D, Shi Y, Tang B, Xu J, Zhong T, Xu W, Zhang J, Zhou J, Ying K, Zhao Y, Sun Y, Jiang Z, Cheng H, Zhang X, Ke Y. SHP2 deneddylation mediates tumor immunosuppression in colon cancer via the CD47/SIRPα axis. J Clin Invest 2023; 133:162870. [PMID: 36626230 PMCID: PMC9927946 DOI: 10.1172/jci162870] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
SIPRα on macrophages binds with CD47 to resist proengulfment signals, but how the downstream signal of SIPRα controls tumor-infiltrating macrophages (TIMs) is still poorly clarified. Here, we report that the CD47/signal regulatory protein α (SIRPα) axis requires the deneddylation of tyrosine phosphatase SHP2. Mechanistically, Src homology region 2-containing protein tyrosine phosphatase 2 (SHP2) was constitutively neddylated on K358 and K364 sites; thus, its autoinhibited conformation was maintained. In response to CD47-liganded SIRPα, SHP2 was deneddylated by sentrin-specific protease 8 (SENP8), which led to the dephosphorylation of relevant substrates at the phagocytic cup and subsequent inhibition of macrophage phagocytosis. Furthermore, neddylation inactivated myeloid-SHP2 and greatly boosted the efficacy of colorectal cancer (CRC) immunotherapy. Importantly, we observed that supplementation with SHP2 allosteric inhibitors sensitized immune treatment-resistant CRC to immunotherapy. Our results emphasize that the CRC subtype that is unresponsive to immunotherapy relies on SIRPαhiSHP2hiNEDD8lo TIMs and highlight the need to further explore the strategy of SHP2 targeting in CRC therapy.
Collapse
Affiliation(s)
- Yiqing Li
- Department of Pathology and Pathophysiology, and Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hui Zhou
- Department of Pathology and Pathophysiology, and Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Pan Liu
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Dandan Lv
- Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yichun Shi
- Department of Pathology and Pathophysiology, and Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bufu Tang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research at The Lishui Hospital, Zhejiang University School of Medicine, Lishui, China
| | - Jiaqi Xu
- Department of Pathology at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangou, China
| | - Tingting Zhong
- Department of Pathology at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangou, China
| | - Wangting Xu
- Department of Respiratory Medicine at The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Zhang
- Department of Urology at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory Medicine at The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kejing Ying
- Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongchao Zhao
- Cancer Institute of The Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Yi Sun
- Cancer Institute of The Second Affiliated Hospital, and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhinong Jiang
- Department of Pathology at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangou, China
| | - Hongqiang Cheng
- Department of Pathology and Pathophysiology, and Department of Cardiology at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xue Zhang
- Department of Pathology and Pathophysiology, and Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yuehai Ke
- Department of Pathology and Pathophysiology, and Department of Respiratory Medicine at Sir Run-Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| |
Collapse
|
5
|
Olaizola P, Lee-Law PY, Fernandez-Barrena MG, Alvarez L, Cadamuro M, Azkargorta M, O'Rourke CJ, Caballero-Camino FJ, Olaizola I, Macias RIR, Marin JJG, Serrano-Maciá M, Martinez-Chantar ML, Avila MA, Aspichueta P, Calvisi DF, Evert M, Fabris L, Castro RE, Elortza F, Andersen JB, Bujanda L, Rodrigues PM, Perugorria MJ, Banales JM. Targeting NAE1-mediated protein hyper-NEDDylation halts cholangiocarcinogenesis and impacts on tumor-stroma crosstalk in experimental models. J Hepatol 2022; 77:177-190. [PMID: 35217064 DOI: 10.1016/j.jhep.2022.02.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 01/13/2022] [Accepted: 02/08/2022] [Indexed: 12/04/2022]
Abstract
BACKGROUND & AIMS Cholangiocarcinoma (CCA) comprises a heterogeneous group of malignant tumors associated with dismal prognosis. Alterations in post-translational modifications (PTMs), including NEDDylation, result in abnormal protein dynamics, cell disturbances and disease. Herein, we investigate the role of NEDDylation in CCA development and progression. METHODS Levels and functions of NEDDylation, together with response to pevonedistat (NEDDylation inhibitor) or CRISPR/Cas9 against NAE1 were evaluated in vitro, in vivo and/or in patients with CCA. The development of preneoplastic lesions in Nae1+/- mice was investigated using an oncogene-driven CCA model. The impact of NEDDylation in CCA cells on tumor-stroma crosstalk was assessed using CCA-derived cancer-associated fibroblasts (CAFs). Proteomic analyses were carried out by mass-spectrometry. RESULTS The NEDDylation machinery was found overexpressed and overactivated in human CCA cells and tumors. Most NEDDylated proteins found upregulated in CCA cells, after NEDD8-immunoprecipitation and further proteomics, participate in the cell cycle, proliferation or survival. Genetic (CRISPR/Cas9-NAE1) and pharmacological (pevonedistat) inhibition of NEDDylation reduced CCA cell proliferation and impeded colony formation in vitro. NEDDylation depletion (pevonedistat or Nae1+/- mice) halted tumorigenesis in subcutaneous, orthotopic, and oncogene-driven models of CCA in vivo. Moreover, pevonedistat potentiated chemotherapy-induced cell death in CCA cells in vitro. Mechanistically, impaired NEDDylation triggered the accumulation of both cullin RING ligase and NEDD8 substrates, inducing DNA damage and cell cycle arrest. Furthermore, impaired NEDDylation in CCA cells reduced the secretion of proteins involved in fibroblast activation, angiogenesis, and oncogenic pathways, ultimately hampering CAF proliferation and migration. CONCLUSION Aberrant protein NEDDylation contributes to cholangiocarcinogenesis by promoting cell survival and proliferation. Moreover, NEDDylation impacts the CCA-stroma crosstalk. Inhibition of NEDDylation with pevonedistat may represent a potential therapeutic strategy for patients with CCA. LAY SUMMARY Little is known about the role of post-translational modifications of proteins in cholangiocarcinoma development and progression. Herein, we show that protein NEDDylation is upregulated and hyperactivated in cholangiocarcinoma, promoting tumor growth. Pharmacological inhibition of NEDDylation halts cholangiocarcinogenesis and could be an effective therapeutic strategy to tackle these tumors.
Collapse
Affiliation(s)
- Paula Olaizola
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Pui Yuen Lee-Law
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain; Department of Gastroenterology & Hepatology, Radboud University Nijmegen Medical Center, The Netherlands
| | - Maite G Fernandez-Barrena
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Hepatology Program, CIMA. University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Laura Alvarez
- Hepatology Program, CIMA. University of Navarra, Pamplona, Spain
| | | | - Mikel Azkargorta
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Colm J O'Rourke
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Francisco J Caballero-Camino
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Irene Olaizola
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain
| | - Rocio I R Macias
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Jose J G Marin
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Experimental Hepatology and Drug Targeting (HEVEPHARM) Group, Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca, Salamanca, Spain
| | - Marina Serrano-Maciá
- Liver Disease Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Spain
| | - Maria L Martinez-Chantar
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Liver Disease Laboratory, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Spain
| | - Matias A Avila
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Hepatology Program, CIMA. University of Navarra, Pamplona, Spain; Instituto de Investigaciones Sanitarias de Navarra (IdiSNA), Pamplona, Spain
| | - Patricia Aspichueta
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Department of Physiology, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; Biocruces Bizkaia Health Research Institute, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Diego F Calvisi
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Matthias Evert
- Institute of Pathology, University of Regensburg, Regensburg, Germany
| | - Luca Fabris
- Department of Molecular Medicine (DMM), University of Padua, Padua, Italy; Department of Internal Medicine, Yale Liver Center (YLC), School of Medicine, Yale University New Haven, CT, USA
| | - Rui E Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Felix Elortza
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Proteomics Platform, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), ProteoRed-ISCIII, Bizkaia Science and Technology Park, Derio, Spain
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luis Bujanda
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain
| | - Pedro M Rodrigues
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain.
| | - Maria J Perugorria
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; Department of Medicine, Faculty of Medicine and Nursing, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain.
| | - Jesus M Banales
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute - Donostia University Hospital -, University of the Basque Country (UPV/EHU), San Sebastian, Spain; National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, "Instituto de Salud Carlos III"), Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain.
| |
Collapse
|
6
|
Arenas V, Castaño JL, Domínguez-García JJ, Yáñez L, Pipaón C. A Different View for an Old Disease: NEDDylation and Other Ubiquitin-Like Post-Translational Modifications in Chronic Lymphocytic Leukemia. Front Oncol 2021; 11:729550. [PMID: 34631557 PMCID: PMC8495217 DOI: 10.3389/fonc.2021.729550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/07/2021] [Indexed: 12/03/2022] Open
Abstract
Despite the enormous amount of molecular data obtained over the years, the molecular etiology of chronic lymphocytic leukemia (CLL) is still largely unknown. All that information has enabled the development of new therapeutic approaches that have improved life expectancy of the patients but are still not curative. We must increase our knowledge of the molecular alterations responsible for the characteristics common to all CLL patients. One of such characteristics is the poor correlation between mRNA and protein expression, that suggests a role of post-translational mechanisms in CLL physiopathology. Drugs targeting these processes have indeed demonstrated an effect either alone or in combination with other aimed at specific pathways. A recent article unveiled an increment in ubiquitin-like modifications in CLL, with many protein members of relevant pathways affected. Interestingly, the inhibition of the NEDD8-activating protein NAE reverted a substantial number of those modifications. The present review gets the scarce data published about the role of NEDDylation in CLL together and establishes connections to what is known from other neoplasias, thus providing a new perspective to the underlying mechanisms in CLL.
Collapse
Affiliation(s)
- Víctor Arenas
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Jose Luis Castaño
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Juan José Domínguez-García
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Lucrecia Yáñez
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| | - Carlos Pipaón
- Laboratorio de Hematología Molecular, Servicio de Hematología, Hospital Universitario Marqués de Valdecilla-Instituto de Investigación Marqués de Valdecilla (IDIVAL), Santander, Spain
| |
Collapse
|
7
|
Ju Z, Wang SY. Prediction of Neddylation Sites Using the Composition of k-spaced Amino Acid Pairs and Fuzzy SVM. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191114123453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Introduction:
Neddylation is the process of ubiquitin-like protein NEDD8 attaching
substrate lysine via isopeptide bonds. As a highly dynamic and reversible post-translational
modification, lysine neddylation has been found to be involved in various biological processes and
closely associated with many diseases.
Objective:
The accurate identification of neddylation sites is necessary to elucidate the underlying
molecular mechanisms of neddylation. As traditional experimental methods are often expensive
and time-consuming, it is imperative to design computational methods to identify neddylation
sites.
Methods:
In this study, a novel predictor named CKSAAP_NeddSite is developed to detect
neddylation sites. An effective feature encoding technology, the composition of k-spaced amino
acid pairs, is used to encode neddylation sites. And the F-score feature selection method is adopted
to remove the redundant features. Moreover, a fuzzy support vector machine algorithm is
employed to overcome the class imbalance and noise problem.
Results:
As illustrated by 10-fold cross-validation, CKSAAP_NeddSite achieves an AUC of
0.9848. Independent tests also show that CKSAAP_NeddSite significantly outperforms existing
neddylation sites predictor. Therefore, CKSAAP_NeddSite can be a useful bioinformatics tool for
the prediction of neddylation sites. Feature analysis shows that some residues around neddylation
sites may play an important role in the prediction.
Conclusion:
The results of analysis and prediction could offer useful information for elucidating
the molecular mechanisms of neddylation. A user-friendly web-server for CKSAAP_NeddSite is
established at 123.206.31.171/CKSAAP_NeddSite.
Collapse
Affiliation(s)
- Zhe Ju
- College of Science, Shenyang Aerospace University, Shenyang 110136, China
| | - Shi-Yun Wang
- College of Science, Shenyang Aerospace University, Shenyang 110136, China
| |
Collapse
|
8
|
Ju Z, Wang SY. Identify Lysine Neddylation Sites Using Bi-profile Bayes Feature Extraction via the Chou's 5-steps Rule and General Pseudo Components. Curr Genomics 2019; 20:592-601. [PMID: 32581647 PMCID: PMC7290059 DOI: 10.2174/1389202921666191223154629] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/19/2019] [Accepted: 11/07/2019] [Indexed: 01/06/2023] Open
Abstract
Introduction Neddylation is a highly dynamic and reversible post-translational modification. The abnormality of neddylation has previously been shown to be closely related to some human diseases. The detection of neddylation sites is essential for elucidating the regulation mechanisms of protein neddylation. Objective As the detection of the lysine neddylation sites by the traditional experimental method is often expensive and time-consuming, it is imperative to design computational methods to identify neddylation sites. Methods In this study, a bioinformatics tool named NeddPred is developed to identify underlying protein neddylation sites. A bi-profile bayes feature extraction is used to encode neddylation sites and a fuzzy support vector machine model is utilized to overcome the problem of noise and class imbalance in the prediction. Results Matthew's correlation coefficient of NeddPred achieved 0.7082 and an area under the receiver operating characteristic curve of 0.9769. Independent tests show that NeddPred significantly outperforms existing lysine neddylation sites predictor NeddyPreddy. Conclusion Therefore, NeddPred can be a complement to the existing tools for the prediction of neddylation sites. A user-friendly webserver for NeddPred is accessible at 123.206.31.171/NeddPred/.
Collapse
Affiliation(s)
- Zhe Ju
- College of Science, Shenyang Aerospace University, Shenyang110136, P.R. China
| | - Shi-Yun Wang
- College of Science, Shenyang Aerospace University, Shenyang110136, P.R. China
| |
Collapse
|
9
|
Maurya S, Mary B, Jayandharan GR. Rational Engineering and Preclinical Evaluation of Neddylation and SUMOylation Site Modified Adeno-Associated Virus Vectors in Murine Models of Hemophilia B and Leber Congenital Amaurosis. Hum Gene Ther 2019; 30:1461-1476. [PMID: 31642343 PMCID: PMC6919284 DOI: 10.1089/hum.2019.164] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Synthetic engineering of viral vectors such as adeno-associated virus (AAV) is crucial to overcome host transduction barriers observed during clinical gene therapy. We reasoned that exploring the role of cellular ubiquitin-like modifiers (UBLs) such as Neddylation or SUMOylation during AAV transduction could be beneficial. Using a combination of in silico biochemical and molecular engineering strategies, we have studied the impact of these UBLs during AAV2 infection and further developed Neddylation or SUMOylation site–modified AAV vectors and validated them in multiple disease models in vitro and in vivo. Hepatic gene transfer of two novel vectors developed, K105Q (SUMOylation-site mutant) and K665Q (Neddylation-site mutant), demonstrated a significantly improved human coagulation factor (F) IX expression (up to two-fold) in a murine model of hemophilia B. Furthermore, subretinal gene transfer of AAV2-K105Q vector expressing RPE65 gene demonstrated visual correction in a murine model of a retinal degenerative disease (rd12 mice). These vectors did not have any adverse immunogenic events in vivo. Taken together, we demonstrate that gene delivery vectors specifically engineered at UBLs can improve the therapeutic outcome during AAV-mediated ocular or hepatic gene therapy.
Collapse
Affiliation(s)
- Shubham Maurya
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Bertin Mary
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| | - Giridhara R Jayandharan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh, India
| |
Collapse
|
10
|
Khalid Z, Sezerman OU. Prediction of HIV Drug Resistance by Combining Sequence and Structural Properties. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:966-973. [PMID: 27992346 DOI: 10.1109/tcbb.2016.2638821] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Drug resistance is a major obstacle faced by therapist in treating HIV infected patients. The reason behind these phenomena is either protein mutation or the changes in gene expression level that induces resistance to drug treatments. These mutations affect the drug binding activity, hence resulting in failure of treatment. Therefore, it is necessary to conduct resistance testing in order to carry out HIV effective therapy. This study combines both sequence and structural features for predicting HIV resistance by applying SVM and Random Forests classifiers. The model was tested on the mutants of HIV-1 protease and reverse transcriptase. Taken together the features we have used in our method, total contact energies among multiple mutations have a strong impact in predicting resistance as they are crucial in understanding the interactions of HIV mutants. The combination of sequence-structure features offers high accuracy with support vector machines as compared to Random Forests classifier. Both single and acquisition of multiple mutations are important in predicting HIV resistance to certain drug treatments. We have discovered the practicality of these features; hence, these can be used in the future to predict resistance for other complex diseases.
Collapse
|
11
|
Li Z, Cui Q, Wang X, Li B, Zhao D, Xia Q, Zhao P. Functions and substrates of NEDDylation during cell cycle in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 90:101-112. [PMID: 28964913 DOI: 10.1016/j.ibmb.2017.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 06/07/2023]
Abstract
NEDDylation, a post-translational modification mediated by the conjugation of the ubiquitin-like protein Nedd8 to specific substrates, is an essential biological process that regulates cell cycle progression in eukaryotes. Here, we report the conservation of NEDDylation machinery and NEDDylated proteins in the silkworm, Bombyx mori. We have identified all the components necessary for reversible NEDDylation in the silkworm including Nedd8, E1, E2, E3, and deNEDDylation enzymes. By the approach of RNAi-mediated gene silencing, it was shown that knockdown of BmNedd8 and the conjugating enzymes decreased the global level of NEDDylation, while knockdown of deNEDDylation enzymes increased the prevalence of this modification in cultured silkworm cells. Moreover, the lack of the NEDDylation system caused cell cycle arrest at the G2/M phase and resulted in defects in chromosome congression and segregation. Using the wild-type and mutants of BmNedd8, we identified the specific substrates of BmNedd8, which are involved in the regulation for many cellular processes, including ribosome biogenesis, spliceosome structure, spindle formation, metabolism, and RNA biogenesis. This clearly demonstrates that the NEDDylation system is able to control multiple pathways in the silkworm. Altogether, the information on the functions and substrates of the NEDDylation system presented here could provide a basis for future investigations of protein NEDDylation and its regulatory mechanism on cell cycle progression in the silkworm.
Collapse
Affiliation(s)
- Zhiqing Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing, China
| | - Qixin Cui
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Xiaoyan Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Bingqian Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Dongchao Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing, China
| | - Ping Zhao
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China; Chongqing Engineering and Technology Research Center for Novel Silk Materials, Chongqing, China.
| |
Collapse
|
12
|
Schönbach C, Horton P, Yiu SM, Tan TW, Ranganathan S. GIW and InCoB are advancing bioinformatics in the Asia-Pacific. BMC Bioinformatics 2015; 16:I1. [PMID: 28102114 PMCID: PMC6389036 DOI: 10.1186/1471-2105-16-s18-i1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
GIW/InCoB2015 the joint 26th International Conference on Genome Informatics (GIW) and 14th International Conference on Bioinformatics (InCoB) held in Tokyo, September 9-11, 2015 was attended by over 200 delegates. Fifty-one out of 89 oral presentations were based on research articles accepted for publication in four BMC journal supplements and three other journals. Sixteen articles in this supplement and six articles in the BMC Systems Biology GIW/InCoB2015 Supplement are covered by this introduction. The topics range from genome informatics, protein structure informatics, image analysis to biological networks and biomarker discovery.
Collapse
Affiliation(s)
- Christian Schönbach
- Department of Biology, School of Science and Technology, Nazarbayev University, Astana, 010000 Republic of Kazakhstan
- Center for AIDS Research and International Research Center for Medical Sciences, Kumamoto University, Kumamoto, 860-0811 Japan
| | - Paul Horton
- Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, 135-0064 Japan
- Department of Computational Biology, Graduate School of Frontier Sciences, University of Tokyo, Japan
| | - Siu-Ming Yiu
- Department of Computer Science, Faculty of Engineering, The University of Hong Kong, Hong Kong, HKSAR
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599
| | - Shoba Ranganathan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109 Australia
| |
Collapse
|